Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold253
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2064896
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 10 of 13
Found at i:1265938 original size:15 final size:15
Alignment explanation
Indices: 1265898--1265941 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1265888 TTCAATTTTA
*
1265898 ACATAAAAT-AATAT
1 ACATAAAATAAAAAT
* *
1265912 AAATATAATAAAAAT
1 ACATAAAATAAAAAT
1265927 ACATAAAATAAAAAT
1 ACATAAAATAAAAAT
1265942 TAAAACAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (15 bp):
ACATAAAATAAAAAT
Found at i:1266312 original size:16 final size:18
Alignment explanation
Indices: 1266274--1266324 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
1266264 ATTTGATCTA
*
1266274 ATAAATTTAATTTAATTT
1 ATAAATTTAATATAATTT
1266292 A-AAATTTAA-AT-ATTT
1 ATAAATTTAATATAATTT
*
1266307 ATAAA-TTAATTTAATTT
1 ATAAATTTAATATAATTT
1266324 A
1 A
1266325 ATTTAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 9 0.32
16 5 0.18
17 13 0.46
18 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATAAATTTAATATAATTT
Found at i:1266334 original size:4 final size:5
Alignment explanation
Indices: 1266277--1266332 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
1266267 TGATCTAATA
* * *
1266277 AATTT AATTT AATTT AAAATTT AA-AT ATTTAT AAATT AATTT AATTT
1 AATTT AATTT AATTT --AATTT AATTT AATT-T AATTT AATTT AATTT
1266324 AATTT AATT
1 AATTT AATT
1266333 AAAATTATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
4 2 0.05
5 31 0.76
6 3 0.07
7 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
AATTT
Found at i:1266347 original size:37 final size:36
Alignment explanation
Indices: 1266277--1266347 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
1266267 TGATCTAATA
*
1266277 AATTTAATTTAATTTAAAATTTAAATATTTATAAATT
1 AATTTAATTTAATTT-AAATTAAAATATTTATAAATT
1266314 AATTTAATTTAATTT-AATTAAAATTATTATATAA
1 AATTTAATTTAATTTAAATTAAAA-TATT-TATAA
1266348 TAATAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 7 0.23
36 4 0.13
37 20 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
AATTTAATTTAATTTAAATTAAAATATTTATAAATT
Found at i:1268023 original size:2 final size:2
Alignment explanation
Indices: 1268016--1268043 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1268006 GCCAAGTAAA
1268016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1268044 GTAAGTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1269999 original size:14 final size:15
Alignment explanation
Indices: 1269973--1270001 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1269963 AAAGAATTAC
1269973 AAAATTAACAACAAA
1 AAAATTAACAACAAA
1269988 AAAATTAA-AACAAA
1 AAAATTAACAACAAA
1270002 TTATTGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAATTAACAACAAA
Found at i:1271874 original size:2 final size:2
Alignment explanation
Indices: 1271869--1271897 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1271859 TACATGTGTG
1271869 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1271898 GGTTAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1272957 original size:29 final size:28
Alignment explanation
Indices: 1272923--1272998 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 28
1272913 TATTTCATTT
* *
1272923 AAAATAATAATTTATTTGAATATAAATTA
1 AAAATAATAATTTATTTAAATAT-AATAA
1272952 AAAATAA-AATTTTATTTAAATATAATAA
1 AAAATAATAA-TTTATTTAAATATAATAA
*
1272980 AAATATAATAATATATTTA
1 AAA-ATAATAATTTATTTA
1272999 TTAAAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 9 0.22
29 30 0.73
30 2 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (28 bp):
AAAATAATAATTTATTTAAATATAATAA
Found at i:1280264 original size:10 final size:10
Alignment explanation
Indices: 1280249--1280363 Score: 50
Period size: 10 Copynumber: 12.0 Consensus size: 10
1280239 TTTTTTATTT
1280249 ATATTTTATA
1 ATATTTTATA
*
1280259 ATATTTTAAA
1 ATATTTTATA
** *
1280269 ATA-TAAATT
1 ATATTTTATA
1280278 ATATTTT-TA
1 ATATTTTATA
1280287 A-ATTTTAATA
1 ATATTTT-ATA
**
1280297 ATA-AATATA
1 ATATTTTATA
1280306 A-ATTTTA-A
1 ATATTTTATA
* *
1280314 A-AATAT-TA
1 ATATTTTATA
1280322 ATAATTTTATA
1 AT-ATTTTATA
*
1280333 ATATTTTATT
1 ATATTTTATA
1280343 ATATTTTAATTA
1 ATATTTT-A-TA
1280355 AT-TTTTATA
1 ATATTTTATA
1280364 TTTATATAAT
Statistics
Matches: 76, Mismatches: 18, Indels: 23
0.65 0.15 0.20
Matches are distributed among these distances:
8 13 0.17
9 15 0.20
10 35 0.46
11 10 0.13
12 3 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATATTTTATA
Found at i:1280382 original size:27 final size:25
Alignment explanation
Indices: 1280352--1280417 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 25
1280342 TATATTTTAA
*
1280352 TTAATTTTTATATTTATATAATTATAT
1 TTAATTTTTAAATTTA-A-AATTATAT
*
1280379 TTAATATTATCAAATTTAAAATTATAT
1 TTAAT-TT-TTAAATTTAAAATTATAT
*
1280406 TTATTTTTTAAA
1 TTAATTTTTAAA
1280418 AAAATTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 4 0.12
26 2 0.06
27 17 0.52
28 3 0.09
29 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTAATTTTTAAATTTAAAATTATAT
Found at i:1286523 original size:2 final size:2
Alignment explanation
Indices: 1286516--1286540 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1286506 GTTGAATTGA
1286516 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1286541 GCTGTATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1291389 original size:22 final size:23
Alignment explanation
Indices: 1291346--1291391 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1291336 TAAATGTTAA
1291346 TTAAAAATTATTTAATTATTATTT
1 TTAAAAA-TATTTAATTATTATTT
1291370 TTAAAAA-ATTTATATT-TTATTT
1 TTAAAAATATTTA-ATTATTATTT
1291392 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 11 0.52
23 3 0.14
24 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTAAAAATATTTAATTATTATTT
Found at i:1291657 original size:27 final size:27
Alignment explanation
Indices: 1291627--1291687 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1291617 CAATATTTTT
1291627 TAAAATTATTTAATATAAT-AATAATAA
1 TAAAATTATTTAATATAATAAATAA-AA
* *
1291654 TAAAATT-GTTAATTTAATAAATAAAA
1 TAAAATTATTTAATATAATAAATAAAA
1291680 -AAAATTAT
1 TAAAATTAT
1291688 CACATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 6 0.21
26 11 0.38
27 12 0.41
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAAATTATTTAATATAATAAATAAAA
Found at i:1293814 original size:2 final size:2
Alignment explanation
Indices: 1293809--1293850 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1293799 AAATCAAGAG
*
1293809 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1293851 TTTCTAACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1295978 original size:17 final size:17
Alignment explanation
Indices: 1295954--1296008 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
1295944 TTCGGAGTTT
1295954 AATTTTTTTT-AATTTA
1 AATTTTTTTTAAATTTA
*
1295970 AATTTTTTTAAAATTTTA
1 AATTTTTTTTAAA-TTTA
**
1295988 AATTAATTTTAAATTTA
1 AATTTTTTTTAAATTTA
1296005 AATT
1 AATT
1296009 AATTAAGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 9 0.27
17 10 0.30
18 14 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTTTTTTTAAATTTA
Found at i:1296009 original size:17 final size:17
Alignment explanation
Indices: 1295959--1296012 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
1295949 AGTTTAATTT
* *
1295959 TTTTTAATTTAAATT-T
1 TTTTAAATTTAAATTAA
1295975 TTTTAAAATTTTAAATTAA
1 TTTT-AAA-TTTAAATTAA
1295994 TTTTAAATTTAAATTAA
1 TTTTAAATTTAAATTAA
1296011 TT
1 TT
1296013 AAGTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 4 0.12
17 14 0.42
18 11 0.33
19 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAAATTTAAATTAA
Found at i:1296037 original size:30 final size:29
Alignment explanation
Indices: 1295962--1296048 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 29
1295952 TTAATTTTTT
*
1295962 TTAA-TTTAAATTTTTTTAAAATT--TTAAA
1 TTAATTTTAAA-TTTTTT-AAATTAATTAAG
1295990 TTAATTTTAAA---TTTAAATTAATTAAG
1 TTAATTTTAAATTTTTTAAATTAATTAAG
1296016 TTAATTTTTAAATTTTTTAAA-TAATATAAG
1 TTAA-TTTTAAATTTTTTAAATTAAT-TAAG
1296046 TTA
1 TTA
1296049 TTTAAGGATT
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
24 5 0.10
25 3 0.06
26 8 0.16
27 7 0.14
28 4 0.08
29 10 0.20
30 13 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
TTAATTTTAAATTTTTTAAATTAATTAAG
Found at i:1296125 original size:15 final size:15
Alignment explanation
Indices: 1296090--1296177 Score: 61
Period size: 16 Copynumber: 5.7 Consensus size: 15
1296080 AGAATTAATG
*
1296090 TTTTTAAATTTTAAT
1 TTTTTAAATTTAAAT
*
1296105 TGTTTTAGATTTAAAT
1 T-TTTTAAATTTAAAT
* *
1296121 TTTTTATATTCAAAT
1 TTTTTAAATTTAAAT
* * *
1296136 ATTTTAAAATATAAAAA
1 -TTTTTAAAT-TTAAAT
*
1296153 TTTTTAAATTTTAA-
1 TTTTTAAATTTAAAT
*
1296167 TATTTAAATTT
1 TTTTTAAATTT
1296178 TTTATTAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
14 10 0.17
15 16 0.28
16 28 0.48
17 4 0.07
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (15 bp):
TTTTTAAATTTAAAT
Found at i:1297332 original size:25 final size:23
Alignment explanation
Indices: 1297317--1297374 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 23
1297307 AATTTTATAT
*
1297317 TAATATTTTATAATTAAATTTAAA
1 TAATAATTTA-AATTAAATTTAAA
*
1297341 TAATAATTTAAATTATA-TTAAA
1 TAATAATTTAAATTAAATTTAAA
1297363 T--TAATTTAAATT
1 TAATAATTTAAATT
1297375 TTATAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.34
22 6 0.19
23 6 0.19
24 9 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAATAATTTAAATTAAATTTAAA
Found at i:1297363 original size:10 final size:10
Alignment explanation
Indices: 1297323--1297374 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 10
1297313 ATATTAATAT
1297323 TTTATAATTAAA
1 TTTA-AATT-AA
1297335 TTTAAATAATAA
1 TTTAAAT--TAA
1297347 TTTAAATT-A
1 TTTAAATTAA
1297356 TATTAAATTAA
1 T-TTAAATTAA
1297367 TTTAAATT
1 TTTAAATT
1297375 TTATAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.06
10 15 0.42
11 5 0.14
12 13 0.36
13 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTAAATTAA
Found at i:1297367 original size:23 final size:25
Alignment explanation
Indices: 1297304--1297367 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 25
1297294 TTATTAAAAT
* * *
1297304 ATTAATTTTATATTAATATTTTATA
1 ATTAAATTTAAATTAATAATTTATA
1297329 ATTAAATTTAAA-TAATAATTTA-A
1 ATTAAATTTAAATTAATAATTTATA
*
1297352 ATTATA-TTAAATTAAT
1 ATTAAATTTAAATTAAT
1297368 TTAAATTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 5 0.15
23 10 0.29
24 9 0.26
25 10 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTAAATTTAAATTAATAATTTATA
Found at i:1301446 original size:2 final size:2
Alignment explanation
Indices: 1301439--1301474 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1301429 AGGAAGGCAA
1301439 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1301475 TATTGATACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1301599 original size:9 final size:10
Alignment explanation
Indices: 1301585--1301621 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
1301575 AAAGAACACC
1301585 AAAAAAAATA
1 AAAAAAAATA
1301595 AAAAAAAATA
1 AAAAAAAATA
1301605 AAAAGAAAATA
1 AAAA-AAAATA
1301616 AGAAAA
1 A-AAAA
1301622 TTAAATGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 14 0.56
11 8 0.32
12 3 0.12
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.08
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:1304726 original size:23 final size:23
Alignment explanation
Indices: 1304692--1304735 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1304682 TCCTATTACT
1304692 TTTAATAATT-AATATTTAATAAA
1 TTTAATAATTAAATA-TTAATAAA
1304715 TTTAA-AATTTAAATATTAATA
1 TTTAATAA-TTAAATATTAATA
1304736 TCGATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 2 0.11
23 13 0.68
24 4 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTAATAATTAAATATTAATAAA
Found at i:1305962 original size:5 final size:5
Alignment explanation
Indices: 1305942--1306038 Score: 53
Period size: 5 Copynumber: 20.2 Consensus size: 5
1305932 TTATATGTAA
* * **
1305942 AATAT AAAAT -ATAT AATAT AATAT GATAT AA-AT -ATAT AAT-T TTTA-
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * * * *
1305987 AAT-T TATAT AATAT AAAAT ATTTT AAATAT AATTAT AATAT AATAA AATAT
1 AATAT AATAT AATAT AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT
1306038 A
1 A
1306039 TAAATTATCA
Statistics
Matches: 66, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
3 1 0.02
4 12 0.18
5 45 0.68
6 8 0.12
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:1305995 original size:25 final size:25
Alignment explanation
Indices: 1305967--1306029 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
1305957 ATATAATATG
*
1305967 ATATAAATATATAAT-TTTTAAATTT
1 ATAT-AATATAAAATATTTTAAATTT
*
1305992 ATATAATATAAAATATTTTAAATATA
1 ATATAATATAAAATATTTTAAAT-TT
1306018 ATTATAATATAA
1 A-TATAATATAA
1306030 TAAAATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 9 0.27
25 12 0.36
26 2 0.06
27 10 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATATAATATAAAATATTTTAAATTT
Found at i:1306043 original size:54 final size:54
Alignment explanation
Indices: 1305942--1306044 Score: 122
Period size: 54 Copynumber: 1.9 Consensus size: 54
1305932 TTATATGTAA
* * *
1305942 AATATAAAATATATAATATAATATGATATAAATATATAATTTTTAAATTTATAT
1 AATATAAAATATATAATATAATATAATATAAATATATAATATATAAATTTATAT
*
1305996 AATATAAAATATTTTAAATATAATTATAATAT-AATA-A-AATATATAAATT
1 AATATAAAATA-TAT-AATATAA-TATAATATAAATATATAATATATAAATT
1306045 ATCACATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
54 21 0.50
55 3 0.07
56 11 0.26
57 7 0.17
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (54 bp):
AATATAAAATATATAATATAATATAATATAAATATATAATATATAAATTTATAT
Found at i:1306807 original size:12 final size:12
Alignment explanation
Indices: 1306786--1306823 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1306776 TTACTGTCTC
1306786 TTTTTT-TTTTT
1 TTTTTTCTTTTT
*
1306797 TTTTTTCTTTTC
1 TTTTTTCTTTTT
1306809 TTTTTTCTTATTT
1 TTTTTTCTT-TTT
1306822 TT
1 TT
1306824 CATACACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 6 0.26
12 13 0.57
13 4 0.17
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:1315188 original size:20 final size:20
Alignment explanation
Indices: 1315152--1315190 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1315142 TAGGTTTAAT
1315152 ATTTGTATTAATATATATAA
1 ATTTGTATTAATATATATAA
*
1315172 ATTT-TATTATATTTATATA
1 ATTTGTATTA-ATATATATA
1315191 TTAATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTGTATTAATATATATAA
Found at i:1315201 original size:26 final size:26
Alignment explanation
Indices: 1315172--1315258 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 26
1315162 ATATATATAA
1315172 ATTTTATTATATTTATATATTAATTT
1 ATTTTATTATATTTATATATTAATTT
1315198 ATTTTTATATATATTT-TA-ATT-ATTT
1 A-TTTTAT-TATATTTATATATTAATTT
** *
1315223 -TTAAAATATATTTATACTATATAATTAT
1 ATTTTATTATATTTATA-TAT-TAATT-T
1315251 ATTTTATT
1 ATTTTATT
1315259 TAATATTGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
22 7 0.15
23 5 0.11
25 6 0.13
26 5 0.11
27 11 0.24
28 8 0.17
29 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTTATTATATTTATATATTAATTT
Found at i:1315210 original size:22 final size:22
Alignment explanation
Indices: 1315162--1315234 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
1315152 ATTTGTATTA
* *
1315162 ATATATATAAATTT-TATTATAT
1 ATATATATTAATTTAT-TTTTAT
*
1315184 TTATATATTAATTTATTTTTAT
1 ATATATATTAATTTATTTTTAT
*
1315206 ATATATTTTAA-TTATTTTTA-
1 ATATATATTAATTTATTTTTAT
*
1315226 AAATATATT
1 ATATATATT
1315235 TATACTATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 7 0.16
21 9 0.21
22 26 0.60
23 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATATATTAATTTATTTTTAT
Found at i:1315213 original size:16 final size:18
Alignment explanation
Indices: 1315178--1315262 Score: 58
Period size: 18 Copynumber: 5.0 Consensus size: 18
1315168 ATAAATTTTA
1315178 TTATATTTATATATTAAT
1 TTATATTTATATATTAAT
*
1315196 TTATTTTTATATA-T-AT
1 TTATATTTATATATTAAT
* * *
1315212 TT-TAATTAT-TTTTAAA
1 TTATATTTATATATTAAT
*
1315228 ATATATTTATACTATATAA-
1 TTATATTTATA-TAT-TAAT
1315247 TTATATTT-TAT-TTAAT
1 TTATATTTATATATTAAT
1315263 ATTGTTCAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
14 1 0.02
15 9 0.18
16 7 0.14
17 8 0.16
18 14 0.27
19 9 0.18
20 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTTATATATTAAT
Found at i:1315727 original size:2 final size:2
Alignment explanation
Indices: 1315722--1315747 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1315712 AGATTTTTTA
1315722 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1315748 TTCTTGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1315905 original size:24 final size:25
Alignment explanation
Indices: 1315861--1315909 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1315851 ATAATTATAT
1315861 AAATATAATATGTATAAAAATATTA
1 AAATATAATATGTATAAAAATATTA
*
1315886 AAATATAATATG-ATATAAATATTA
1 AAATATAATATGTATAAAAATATTA
1315910 TGTTCGGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (25 bp):
AAATATAATATGTATAAAAATATTA
Found at i:1320817 original size:30 final size:30
Alignment explanation
Indices: 1320783--1320842 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1320773 CGTTTGGCAC
1320783 TAAGTTCCAAGTCCAACCCAACTTCAACAG
1 TAAGTTCCAAGTCCAACCCAACTTCAACAG
1320813 TAAGTTCCAAGTCCAACCCAACTTCAACAG
1 TAAGTTCCAAGTCCAACCCAACTTCAACAG
1320843 GCAGGTCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.20
Consensus pattern (30 bp):
TAAGTTCCAAGTCCAACCCAACTTCAACAG
Found at i:1321495 original size:15 final size:15
Alignment explanation
Indices: 1321475--1321508 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1321465 ATGACCATCA
1321475 TCAGCTACAACCATT
1 TCAGCTACAACCATT
*
1321490 TCAGCTACAGCCATT
1 TCAGCTACAACCATT
1321505 TCAG
1 TCAG
1321509 AATCCTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (15 bp):
TCAGCTACAACCATT
Found at i:1323464 original size:17 final size:17
Alignment explanation
Indices: 1323438--1323481 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1323428 AATTTGAAAA
*
1323438 AAATAAATATTAAATAT
1 AAATATATATTAAATAT
* *
1323455 GAATATATATTATATAT
1 AAATATATATTAAATAT
1323472 AAATATATAT
1 AAATATATAT
1323482 GTGATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AAATATATATTAAATAT
Found at i:1325375 original size:2 final size:2
Alignment explanation
Indices: 1325368--1325393 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1325358 ATATACAAAC
1325368 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1325394 TAATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1326434 original size:27 final size:27
Alignment explanation
Indices: 1326382--1326440 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
1326372 GCTTTTAATA
* *
1326382 TAATTTAATTATGATTATAAATAATTT
1 TAATTTAAATATGATTAAAAATAATTT
* *
1326409 TAATTTAAATAT-TTTAAAAATAAATT
1 TAATTTAAATATGATTAAAAATAATTT
*
1326435 TGATTT
1 TAATTT
1326441 TTTATAAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (27 bp):
TAATTTAAATATGATTAAAAATAATTT
Found at i:1326559 original size:33 final size:36
Alignment explanation
Indices: 1326470--1326559 Score: 82
Period size: 33 Copynumber: 2.5 Consensus size: 36
1326460 ATGATGATTG
*
1326470 AATAATAATTAATTTTTGTATACAAATTTAAATCATTT
1 AATAATAATTAA-TTTTATATACAAATTTAAA-CATTT
* *
1326508 AA-AATAACTTTAA-ATTATATA-ACATTT-AA-ATTT
1 AATAATAA--TTAATTTTATATACAAATTTAAACATTT
1326541 AATAATAATTAATTTTATA
1 AATAATAATTAATTTTATA
1326560 AAAAATTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
32 4 0.09
33 11 0.25
34 5 0.11
35 2 0.05
36 5 0.11
37 11 0.25
38 2 0.05
39 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (36 bp):
AATAATAATTAATTTTATATACAAATTTAAACATTT
Found at i:1326575 original size:20 final size:22
Alignment explanation
Indices: 1326546--1326603 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
1326536 AATTTAATAA
* *
1326546 TAATTAATTTTATAAAAA-A-T
1 TAATTTATTTTTTAAAAATATT
1326566 TAATTTATTTTTTAAAAATATT
1 TAATTTATTTTTTAAAAATATT
*
1326588 TAAATTATTTTTTAAA
1 TAATTTATTTTTTAAA
1326604 TTATATATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 16 0.48
21 1 0.03
22 16 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATTTATTTTTTAAAAATATT
Found at i:1326609 original size:23 final size:22
Alignment explanation
Indices: 1326547--1326603 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
1326537 ATTTAATAAT
*
1326547 AATTAATTTTATAAAAA-A-TTA
1 AATT-ATTTTTTAAAAATATTTA
*
1326568 ATTTATTTTTTAAAAATATTTA
1 AATTATTTTTTAAAAATATTTA
1326590 AATTATTTTTTAAA
1 AATTATTTTTTAAA
1326604 TTATATATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.35
21 4 0.13
22 16 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTATTTTTTAAAAATATTTA
Found at i:1334593 original size:23 final size:23
Alignment explanation
Indices: 1334567--1334616 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
1334557 TTTTATAAAA
*
1334567 TTAATAT-ATTAAATGTAAATTTT
1 TTAATATGA-TAAATGAAAATTTT
1334590 TTAA-ATGATAAATGAAAATTTT
1 TTAATATGATAAATGAAAATTTT
1334612 TTAAT
1 TTAAT
1334617 TAATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (23 bp):
TTAATATGATAAATGAAAATTTT
Found at i:1334683 original size:39 final size:39
Alignment explanation
Indices: 1334597--1334703 Score: 116
Period size: 37 Copynumber: 2.7 Consensus size: 39
1334587 TTTTTAAATG
*
1334597 ATAAATGA-AAATTTTTTAATTAATATTTATAAATATATA
1 ATAAAT-ATAAATTTTTTAATAAATATTTATAAATATATA
1334636 AT-AA-ATAAATTTTTTAA-AAATTATATT-TAAATATATA
1 ATAAATATAAATTTTTTAATAAA-TAT-TTATAAATATATA
*
1334673 ATAAATATAAATATTTTTATTAAATAATTTA
1 ATAAATATAAAT-TTTTTAATAAAT-ATTTA
1334704 AAGATCATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
36 3 0.05
37 26 0.46
38 6 0.11
39 8 0.14
40 9 0.16
41 5 0.09
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (39 bp):
ATAAATATAAATTTTTTAATAAATATTTATAAATATATA
Found at i:1335506 original size:11 final size:12
Alignment explanation
Indices: 1335483--1335516 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1335473 TACAAATAAG
1335483 ATATAAAAAATA
1 ATATAAAAAATA
*
1335495 AT-TAAAATATA
1 ATATAAAAAATA
1335506 ATATAAAAAAT
1 ATATAAAAAAT
1335517 TACATAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
ATATAAAAAATA
Found at i:1337362 original size:20 final size:19
Alignment explanation
Indices: 1337325--1337363 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1337315 TTACATATGT
* *
1337325 TTTAATATTTATATTATAA
1 TTTAAAATTTATAATATAA
1337344 TTTAAAATTATATAATATAA
1 TTTAAAATT-TATAATATAA
1337364 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAAAATTTATAATATAA
Found at i:1339210 original size:14 final size:16
Alignment explanation
Indices: 1339191--1339225 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
1339181 AATTTTTATC
1339191 AATAATAA-ATG-TAA
1 AATAATAAGATGTTAA
1339205 AATAATAAGATGTTAA
1 AATAATAAGATGTTAA
1339221 AATAA
1 AATAA
1339226 AAAAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
15 3 0.16
16 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.29
Consensus pattern (16 bp):
AATAATAAGATGTTAA
Found at i:1340174 original size:15 final size:17
Alignment explanation
Indices: 1340146--1340177 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1340136 TAATTAATTG
1340146 ATATTTAATAAATTTTA
1 ATATTTAATAAATTTTA
1340163 ATATTT-AT-AATTTTA
1 ATATTTAATAAATTTTA
1340178 TTTTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTAATAAATTTTA
Found at i:1342971 original size:2 final size:2
Alignment explanation
Indices: 1342964--1343000 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1342954 AAACTCAATC
1342964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1343001 GTAAAATTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1343294 original size:16 final size:17
Alignment explanation
Indices: 1343273--1343311 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1343263 GCTAAGACAG
*
1343273 AATATAAAAT-TTTTAT
1 AATATAAAATACTTTAT
1343289 AATATAAAATACTTTAT
1 AATATAAAATACTTTAT
1343306 -ATATAA
1 AATATAA
1343312 TTTTTTACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATAAAATACTTTAT
Found at i:1343645 original size:18 final size:19
Alignment explanation
Indices: 1343614--1343651 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1343604 AATTATCGAA
1343614 TAATTATTAATT-AATATT
1 TAATTATTAATTAAATATT
**
1343632 TAATTATTTTTTAAATATT
1 TAATTATTAATTAAATATT
1343651 T
1 T
1343652 TTATATAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TAATTATTAATTAAATATT
Found at i:1344437 original size:22 final size:22
Alignment explanation
Indices: 1344412--1344477 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
1344402 ACAAATATTT
1344412 TTATATAAATTTAATTATAAAA
1 TTATATAAATTTAATTATAAAA
1344434 TTATATAAATATTAA-TATAAAAA
1 TTATATAAAT-TTAATTAT-AAAA
* *
1344457 TAATAATTAATTTAATT-TAAA
1 TTAT-ATAAATTTAATTATAAA
1344478 TTAAAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 16 0.42
23 16 0.42
24 6 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTATATAAATTTAATTATAAAA
Found at i:1344477 original size:23 final size:22
Alignment explanation
Indices: 1344414--1344477 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
1344404 AAATATTTTT
*
1344414 ATATAAATTTAA-TTATAAAATT
1 ATATAAATTTAATTTA-AAAATA
*
1344436 ATATAAATATTAATATAAAAATA
1 ATATAAAT-TTAATTTAAAAATA
*
1344459 ATAATTAATTTAATTTAAA
1 AT-ATAAATTTAATTTAAA
1344478 TTAAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 8 0.23
23 20 0.57
24 7 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATAAATTTAATTTAAAAATA
Found at i:1344501 original size:7 final size:8
Alignment explanation
Indices: 1344482--1344507 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1344472 TTTAAATTAA
1344482 AAAAAATT
1 AAAAAATT
1344490 AAAAAATT
1 AAAAAATT
1344498 AAAAAATT
1 AAAAAATT
1344506 AA
1 AA
1344508 TTTGATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAAATT
Found at i:1351393 original size:2 final size:2
Alignment explanation
Indices: 1351386--1351423 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1351376 TACATGTAAA
1351386 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1351424 CGCATGGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1355263 original size:48 final size:48
Alignment explanation
Indices: 1355192--1355285 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 48
1355182 ATGTGGCTTG
*
1355192 GCAGGAACAGAGGCCTTATAAGTTACAACATCCTTTCGAACATCAGTT
1 GCAGGAACAGAGGCCTTATAAGTTACAACATCCGTTCGAACATCAGTT
* * * ** *
1355240 GCAGGAACTGGGGTCTTATAAGTTGTATCATCCGTTCGAACATCAG
1 GCAGGAACAGAGGCCTTATAAGTTACAACATCCGTTCGAACATCAG
1355286 CAGCATGCTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (48 bp):
GCAGGAACAGAGGCCTTATAAGTTACAACATCCGTTCGAACATCAGTT
Found at i:1358374 original size:13 final size:13
Alignment explanation
Indices: 1358356--1358380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1358346 ATGAGACAGT
1358356 GACAGTGACAGGA
1 GACAGTGACAGGA
1358369 GACAGTGACAGG
1 GACAGTGACAGG
1358381 TAAAGCAGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.40, T:0.08
Consensus pattern (13 bp):
GACAGTGACAGGA
Found at i:1358390 original size:19 final size:19
Alignment explanation
Indices: 1358349--1358391 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1358339 AAAGAGAATG
* *
1358349 AGACAGTGACAGTGACAGG
1 AGACAGTGACAGTGAAAGC
1358368 AGACAGTGACAG-GTAAAGC
1 AGACAGTGACAGTG-AAAGC
1358387 AGACA
1 AGACA
1358392 TTATAGGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.42, C:0.16, G:0.33, T:0.09
Consensus pattern (19 bp):
AGACAGTGACAGTGAAAGC
Found at i:1359946 original size:26 final size:24
Alignment explanation
Indices: 1359917--1359977 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 24
1359907 ATTTTTCGGA
*
1359917 TAAAATTAATAAAATAATATATATTT
1 TAAAATTAATAAAAAAAT-TA-ATTT
*
1359943 TAAAAATAATAAAAAAATTAATTT
1 TAAAATTAATAAAAAAATTAATTT
* *
1359967 AAAAATAAATA
1 TAAAATTAATA
1359978 TGATATACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 12 0.40
25 2 0.07
26 16 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAAATTAATAAAAAAATTAATTT
Found at i:1359951 original size:23 final size:23
Alignment explanation
Indices: 1359924--1359984 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
1359914 GGATAAAATT
*
1359924 AATAAAATAATATATATTTTAAA
1 AATAAAATAATATATAATTTAAA
* *
1359947 AATAATAAAAAAAT-TAATTTAAA
1 AATAA-AATAATATATAATTTAAA
*
1359970 AATAAATATGATATA
1 AATAAA-ATAATATA
1359985 CAATGATCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
22 1 0.03
23 22 0.76
24 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AATAAAATAATATATAATTTAAA
Found at i:1360525 original size:18 final size:18
Alignment explanation
Indices: 1360499--1360547 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1360489 ATTTTACAAT
1360499 TTATATTAAAATATATAA
1 TTATATTAAAATATATAA
* *
1360517 TTATTTTAATATATATAAA
1 TTATATTAAAATATAT-AA
*
1360536 TT-TATAAAAATA
1 TTATATTAAAATA
1360548 ATTAAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATATTAAAATATATAA
Found at i:1360653 original size:15 final size:15
Alignment explanation
Indices: 1360608--1360654 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1360598 AACTTACATT
*
1360608 TTTTTATAATTAAAA
1 TTTTAATAATTAAAA
* *
1360623 TTATAA-AATTTTAAA
1 TTTTAATAA-TTAAAA
1360638 TTTTAATAATTAAAA
1 TTTTAATAATTAAAA
1360653 TT
1 TT
1360655 AAAAATCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
14 2 0.08
15 21 0.84
16 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTAATAATTAAAA
Found at i:1361070 original size:23 final size:24
Alignment explanation
Indices: 1361036--1361098 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
1361026 TATTTTATTA
1361036 TATTATAA-TTATATTTAAAATAT
1 TATTATAATTTATATTTAAAATAT
*
1361059 TA-TATAATTTATATTTAATATAT
1 TATTATAATTTATATTTAAAATAT
*
1361082 TATTAATAGTTTATATT
1 TATT-ATAATTTATATT
1361099 ATATTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 5 0.14
23 18 0.51
24 1 0.03
25 11 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATTATAATTTATATTTAAAATAT
Found at i:1361087 original size:11 final size:11
Alignment explanation
Indices: 1361013--1361089 Score: 56
Period size: 11 Copynumber: 7.2 Consensus size: 11
1361003 GTCGATAGAC
*
1361013 TATATCATTAA
1 TATATTATTAA
*
1361024 TATATT-TTAT
1 TATATTATTAA
1361034 TATATTA-TAA
1 TATATTATTAA
1361044 T-TA-TATTTAA
1 TATATTA-TTAA
*
1361054 AATATTATATAA
1 TATATTAT-TAA
*
1361066 TTTA-TATTTAA
1 TATATTA-TTAA
1361077 TATATTATTAA
1 TATATTATTAA
1361088 TA
1 TA
1361090 GTTTATATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 16
0.69 0.09 0.22
Matches are distributed among these distances:
8 2 0.04
9 2 0.04
10 15 0.29
11 22 0.43
12 10 0.20
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATTATTAA
Found at i:1361105 original size:11 final size:11
Alignment explanation
Indices: 1361024--1361197 Score: 68
Period size: 11 Copynumber: 16.3 Consensus size: 11
1361014 ATATCATTAA
1361024 TATATTT-TAT
1 TATATTTATAT
1361034 TATA-TTATAAT
1 TATATTTAT-AT
1361045 TATATTTA-A-
1 TATATTTATAT
*
1361054 AATA-TTATA-
1 TATATTTATAT
1361063 TA-ATTTATATT
1 TATATTTATA-T
1361074 TAATATATTAT-T
1 T-ATAT-TTATAT
*
1361086 AATAGTTTATAT
1 TATA-TTTATAT
*
1361098 TATATTTATTT
1 TATATTTATAT
1361109 TAATATTT-TA-
1 T-ATATTTATAT
*
1361119 -ATATTTTTAT
1 TATATTTATAT
*
1361129 TATATTAATAT
1 TATATTTATAT
*
1361140 TAT-TTTTTAT
1 TATATTTATAT
* * * *
1361150 CAAATTAAATTT
1 TATATT-TATAT
*
1361162 TATATTTATTT
1 TATATTTATAT
*
1361173 TA-ATTTTTAT
1 TATATTTATAT
*
1361183 TATATATTACAT
1 TATAT-TTATAT
1361195 TAT
1 TAT
1361198 TAAATTTATA
Statistics
Matches: 122, Mismatches: 22, Indels: 38
0.67 0.12 0.21
Matches are distributed among these distances:
8 10 0.08
9 14 0.11
10 20 0.16
11 43 0.35
12 29 0.24
13 2 0.02
14 4 0.03
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1361177 original size:17 final size:17
Alignment explanation
Indices: 1361091--1361208 Score: 59
Period size: 17 Copynumber: 6.8 Consensus size: 17
1361081 TTATTAATAG
*
1361091 TTTATA-TTATATTTAT
1 TTTATATTTATATTAAT
*
1361107 TTTAATATTT-TAAT-AT
1 TTT-ATATTTATATTAAT
1361123 TTT-TA-TTATATTAAT
1 TTTATATTTATATTAAT
* *
1361138 ATTATTTTTTATCAAATTAAAT
1 TTTA-TATTTAT---ATT-AAT
*
1361160 TTTATATTTATTTTAAT
1 TTTATATTTATATTAAT
1361177 TTT-TATTATATATTACAT
1 TTTATATT-TATATTA-AT
*
1361195 TATTAAATTTATAT
1 T-TTATATTTATAT
1361209 ACTAATAATA
Statistics
Matches: 78, Mismatches: 9, Indels: 27
0.68 0.08 0.24
Matches are distributed among these distances:
13 2 0.03
14 5 0.06
15 4 0.05
16 12 0.15
17 19 0.24
18 11 0.14
19 7 0.09
20 3 0.04
21 9 0.12
22 6 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTATATTTATATTAAT
Found at i:1361288 original size:9 final size:9
Alignment explanation
Indices: 1361257--1361311 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
1361247 TATATTAAAT
1361257 AAAT-TATA
1 AAATATATA
*
1361265 ACATA-ATA
1 AAATATATA
1361273 TAAATATATA
1 -AAATATATA
1361283 AAATAT-TA
1 AAATATATA
1361291 AAATTTATATA
1 AAA--TATATA
1361302 AAATATATA
1 AAATATATA
1361311 A
1 A
1361312 TTTTTTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
8 11 0.28
9 17 0.44
10 6 0.15
11 5 0.13
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATATATA
Found at i:1362499 original size:17 final size:19
Alignment explanation
Indices: 1362462--1362504 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
1362452 AAAAATATAA
1362462 AAAATAAATTATAAATGAT
1 AAAATAAATTATAAATGAT
*
1362481 AAAA-AAATTA-AAATTAT
1 AAAATAAATTATAAATGAT
1362498 AAAATAA
1 AAAATAA
1362505 TAATTATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 8 0.36
19 4 0.18
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAAATTATAAATGAT
Found at i:1362518 original size:22 final size:20
Alignment explanation
Indices: 1362457--1362520 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
1362447 TTATGAAAAA
1362457 TATAAAAAATAAATTATAAAT
1 TATAAAAAAT-AATTATAAAT
*
1362478 GAT-AAAAA-AATTA-AAAT
1 TATAAAAAATAATTATAAAT
1362495 TATAAAATAATAATTATAACAT
1 TATAAAA-AATAATTATAA-AT
1362517 TATA
1 TATA
1362521 TTATTATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 6 0.17
18 8 0.22
19 2 0.06
20 10 0.28
21 4 0.11
22 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TATAAAAAATAATTATAAAT
Found at i:1362525 original size:3 final size:3
Alignment explanation
Indices: 1362515--1362558 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1362505 TAATTATAAC
1362515 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1362559 TCAACTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1362730 original size:16 final size:15
Alignment explanation
Indices: 1362703--1362750 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1362693 TATGATACAA
*
1362703 ATATAATAAATTATT
1 ATATAATTAATTATT
*
1362718 ATCATAATTAATTATA
1 AT-ATAATTAATTATT
*
1362734 ATAAATATTAATTATT
1 ATATA-ATTAATTATT
1362750 A
1 A
1362751 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATAATTAATTATT
Found at i:1363046 original size:5 final size:5
Alignment explanation
Indices: 1363036--1363098 Score: 67
Period size: 5 Copynumber: 12.6 Consensus size: 5
1363026 AGTATTGATT
* *
1363036 ATATA ATATAA ATATA ATATA ATAT- ATATA ATTAAA ATATA ATATA ATAAA
1 ATATA ATAT-A ATATA ATATA ATATA ATATA A-TATA ATATA ATATA ATATA
*
1363087 ATA-A AAATA ATA
1 ATATA ATATA ATA
1363099 AAAATATATT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
4 7 0.14
5 33 0.67
6 9 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:1363067 original size:25 final size:25
Alignment explanation
Indices: 1363035--1363084 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1363025 TAGTATTGAT
1363035 TATATAA-TATAAATATAATATAATA
1 TATATAATTA-AAATATAATATAATA
1363060 TATATAATTAAAATATAATATAATA
1 TATATAATTAAAATATAATATAATA
1363085 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TATATAATTAAAATATAATATAATA
Found at i:1363082 original size:30 final size:30
Alignment explanation
Indices: 1363040--1363120 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
1363030 TTGATTATAT
* * *
1363040 AATATAAATATAATATAATATATATAATTAA
1 AATAT-AATATAATATAATAAAAATAATAAA
*
1363071 AATATAATATAATAAAATAAAAATAATAAA
1 AATATAATATAATATAATAAAAATAATAAA
*
1363101 AATAT-AT-TAATATATTAAAA
1 AATATAATATAATATAATAAAA
1363121 TTTATAAGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.25
29 2 0.05
30 26 0.59
31 5 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (30 bp):
AATATAATATAATATAATAAAAATAATAAA
Found at i:1364158 original size:11 final size:11
Alignment explanation
Indices: 1364137--1364187 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
1364127 CTAAATTCGA
1364137 TTATCATTATAT
1 TTAT-ATTATAT
1364149 TTATATTATAT
1 TTATATTATAT
1364160 TTATTATT-T-T
1 TTA-TATTATAT
*
1364170 TT-TATTATAA
1 TTATATTATAT
1364180 TTATATTA
1 TTATATTA
1364188 AAAAATTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
8 4 0.12
9 1 0.03
10 5 0.15
11 16 0.47
12 8 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATATTATAT
Found at i:1364175 original size:20 final size:20
Alignment explanation
Indices: 1364142--1364183 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1364132 TTCGATTATC
*
1364142 ATTATATTTATATTATATTT
1 ATTATATTTATATTATAATT
* *
1364162 ATTATTTTTTTATTATAATT
1 ATTATATTTATATTATAATT
1364182 AT
1 AT
1364184 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTATATTTATATTATAATT
Found at i:1364195 original size:19 final size:19
Alignment explanation
Indices: 1364173--1364217 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
1364163 TTATTTTTTT
1364173 ATTATAATTATATTA-AAAA
1 ATTATAATTAT-TTATAAAA
1364192 ATTA-AA-TATTTATAAAA
1 ATTATAATTATTTATAAAA
*
1364209 ATTTTAATT
1 ATTATAATT
1364218 TGATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
16 3 0.14
17 10 0.45
18 4 0.18
19 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTATAATTATTTATAAAA
Found at i:1364260 original size:24 final size:24
Alignment explanation
Indices: 1364233--1364278 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1364223 ATAATTTATA
1364233 TTATATTATATTTA-ATTAATATTT
1 TTATATTATATTTATA-TAATATTT
1364257 TTATATTATATTTATATAATAT
1 TTATATTATATTTATATAATAT
1364279 AAATTTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATATTATATTTATATAATATTT
Found at i:1364270 original size:11 final size:11
Alignment explanation
Indices: 1364228--1364278 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
1364218 TGATAATAAT
1364228 TTATA-TTATA
1 TTATATTTATA
1364238 TTATATTTA-A
1 TTATATTTATA
1364248 TTAATATTTTTATA
1 TT-ATA--TTTATA
1364262 TTATATTTATA
1 TTATATTTATA
*
1364273 TAATAT
1 TTATAT
1364279 AAATTTATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 8 0.23
11 17 0.49
13 7 0.20
14 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1364650 original size:5 final size:5
Alignment explanation
Indices: 1364623--1364674 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
1364613 AAATATAATC
* *
1364623 ATATA A-ATA ATATA ATTAAA ATATA ATATA ATATG ATATA A-ATA TATATA
1 ATATA ATATA ATATA A-TATA ATATA ATATA ATATA ATATA ATATA -ATATA
1364673 AT
1 AT
1364675 TAAAGTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 7 0.18
5 25 0.64
6 7 0.18
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:1367364 original size:22 final size:22
Alignment explanation
Indices: 1367339--1367380 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1367329 TAGTTTTATT
1367339 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1367361 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1367381 ATATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1367513 original size:5 final size:5
Alignment explanation
Indices: 1367503--1367591 Score: 50
Period size: 5 Copynumber: 19.0 Consensus size: 5
1367493 AATAATTTTA
* *
1367503 AATAT AATAT AAT-T -ATAT AATAT AAAAT -AT-T AATTAA AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT
* * * *
1367550 AACAT AA-AA AATAT -ATAAT AA-AT TATAT AAAAT -ATAT AATAT
1 AATAT AATAT AATAT AAT-AT AATAT AATAT AATAT AATAT AATAT
1367592 TATAAAAAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
3 3 0.05
4 15 0.24
5 42 0.67
6 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:1367516 original size:17 final size:17
Alignment explanation
Indices: 1367494--1367551 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
1367484 TTTAAAATTA
1367494 ATAATTTTAAATATAAT
1 ATAATTTTAAATATAAT
*
1367511 ATAATTATATAATATAAAAT
1 ATAATT-T-TAA-ATATAAT
*
1367531 ATTAA-TTAAAATATAAT
1 A-TAATTTTAAATATAAT
1367548 ATAA
1 ATAA
1367552 CATAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
16 3 0.09
17 13 0.38
18 3 0.09
19 4 0.12
20 8 0.24
21 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTTTAAATATAAT
Found at i:1367540 original size:12 final size:13
Alignment explanation
Indices: 1367502--1367591 Score: 55
Period size: 14 Copynumber: 6.9 Consensus size: 13
1367492 TAATAATTTT
1367502 AAATA-TAATAT-
1 AAATATTAATATA
*
1367513 AATTATATAATATA
1 AAATAT-TAATATA
1367527 AAATATTAAT-TA
1 AAATATTAATATA
1367539 AAATA-TAATATA
1 AAATATTAATATA
* **
1367551 ACATAAAAAATATA
1 AAAT-ATTAATATA
*
1367565 TAATAAATT-ATATA
1 -AA-ATATTAATATA
1367579 AAATATATAATAT
1 AAATAT-TAATAT
1367592 TATAAAAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
11 8 0.13
12 15 0.25
13 14 0.23
14 20 0.33
15 2 0.03
16 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (13 bp):
AAATATTAATATA
Found at i:1367567 original size:21 final size:22
Alignment explanation
Indices: 1367541--1367602 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
1367531 ATTAATTAAA
1367541 ATATAATATAA-CATAAAAAAT
1 ATATAATATAATCATAAAAAAT
* *
1367562 ATATAATA-AATTATATAAAAT
1 ATATAATATAATCATAAAAAAT
1367583 ATATAATAT--T-ATAAAAAAT
1 ATATAATATAATCATAAAAAAT
1367602 A
1 A
1367603 ACACAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 9 0.25
20 3 0.08
21 24 0.67
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
ATATAATATAATCATAAAAAAT
Found at i:1367570 original size:19 final size:18
Alignment explanation
Indices: 1367538--1367602 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 18
1367528 AATATTAATT
1367538 AAAATATA-ATATAACATAA
1 AAAATATATA-ATAA-ATAA
1367557 AAAATATATAATAAATTATA
1 AAAATATATAATAAA-TA-A
*
1367577 TAAAATATATAATATTATAA
1 -AAAATATATAATA-AATAA
1367597 AAAATA
1 AAAATA
1367603 ACACAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
18 1 0.03
19 20 0.50
20 3 0.08
21 15 0.38
22 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATATATAATAAATAA
Found at i:1370196 original size:21 final size:20
Alignment explanation
Indices: 1370156--1370208 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1370146 ATAGCAAGTC
*
1370156 TGTTTTTTTTAATAAGTTTT
1 TGTTTTTCTTAATAAGTTTT
1370176 TGTTTTGTCTTAATTAA-TTTT
1 TGTTTT-TCTTAA-TAAGTTTT
1370197 TGATTTTT-TTAA
1 TG-TTTTTCTTAA
1370209 AAAAATTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 10 0.34
21 12 0.41
22 7 0.24
ACGTcount: A:0.21, C:0.02, G:0.09, T:0.68
Consensus pattern (20 bp):
TGTTTTTCTTAATAAGTTTT
Found at i:1375069 original size:2 final size:2
Alignment explanation
Indices: 1375049--1375087 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1375039 AAGAAAAGAA
* *
1375049 AT AT AA AT AT -T AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1375088 TGTGATTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1381887 original size:27 final size:27
Alignment explanation
Indices: 1381828--1381959 Score: 74
Period size: 27 Copynumber: 4.7 Consensus size: 27
1381818 CATCGATAAC
*
1381828 TATTTAAAATATTTTATATTTATATTA
1 TATTTAAAATATTATATATTTATATTA
*
1381855 -ATTTTAATATATTA-ATAATTTATATTA
1 TA-TTTAAAATATTATAT-ATTTATATTA
*
1381882 TATTTATTTAAATAATATTTATATTT-T-TTA
1 TATTTA---AAAT-AT-TATATATTTATATTA
** *
1381912 TATTATATCATATTATATATTTATTTTAA
1 TATT-TAAAATATTATATATTTATATT-A
***
1381941 TATTTTTTATATTATATAT
1 TATTTAAAATATTATATAT
1381960 AATATTGTCA
Statistics
Matches: 83, Mismatches: 9, Indels: 25
0.71 0.08 0.21
Matches are distributed among these distances:
26 11 0.13
27 27 0.33
28 18 0.22
29 5 0.06
30 10 0.12
31 5 0.06
32 5 0.06
33 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (27 bp):
TATTTAAAATATTATATATTTATATTA
Found at i:1381899 original size:20 final size:19
Alignment explanation
Indices: 1381876--1381925 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1381866 TTAATAATTT
1381876 ATATTATATTTATTTAAATA
1 ATATTATATTT-TTTAAATA
* *
1381896 ATATTTATATTTTTTATATT
1 ATA-TTATATTTTTTAAATA
*
1381916 ATATCATATT
1 ATATTATATT
1381926 ATATATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 6 0.23
20 12 0.46
21 8 0.31
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTATATTTTTTAAATA
Found at i:1381900 original size:33 final size:33
Alignment explanation
Indices: 1381835--1381962 Score: 105
Period size: 38 Copynumber: 3.6 Consensus size: 33
1381825 AACTATTTAA
*
1381835 AATATTTTATATTTATATTAATTTTAATATA-TT
1 AATATTTTATA-TTATATTAATTTAAATATATTT
* *
1381868 AATAATTTATATTATATTTATTTAAATAATATTT
1 AATATTTTATATTATATTAATTTAAAT-ATATTT
* * * *
1381902 ATATTTTTTATATTATATCATATTATATATTTATTTT
1 A-ATATTTTATATTATATTA-ATT-TAAATATA-TTT
1381939 AATATTTTTTATATTATATATAAT
1 AATA--TTTTATATTATAT-TAAT
1381963 ATTGTCATAT
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
32 14 0.19
33 13 0.17
34 3 0.04
35 14 0.19
36 7 0.09
37 8 0.11
38 15 0.20
39 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (33 bp):
AATATTTTATATTATATTAATTTAAATATATTT
Found at i:1381911 original size:24 final size:26
Alignment explanation
Indices: 1381843--1381937 Score: 88
Period size: 26 Copynumber: 3.6 Consensus size: 26
1381833 AAAATATTTT
* * *
1381843 ATATTTATATTAATTT-TAATATATTA
1 ATATTTATATTTATTTATATTA-AATA
1381869 ATAATTTATATTATATTTAT-TTAAATA
1 AT-ATTTATATT-TATTTATATTAAATA
* *
1381896 ATATTTATATTT-TTTATATTATATC
1 ATATTTATATTTATTTATATTAAATA
1381921 ATATTATATATTTATTT
1 ATATT-TATATTTATTT
1381938 TAATATTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
24 5 0.09
25 11 0.19
26 18 0.31
27 17 0.29
28 6 0.10
29 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (26 bp):
ATATTTATATTTATTTATATTAAATA
Found at i:1381962 original size:21 final size:21
Alignment explanation
Indices: 1381875--1381965 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 21
1381865 ATTAATAATT
* * *
1381875 TATATTATATTTATTTAAATAA
1 TATATAATATTT-TTTATATTA
*
1381897 TAT-TTATATTTTTTATA-T-
1 TATATAATATTTTTTATATTA
* * *
1381915 TATATCATATTATATAT-TTA
1 TATATAATATTTTTTATATTA
*
1381935 T-TTTAATATTTTTTATATTA
1 TATATAATATTTTTTATATTA
1381955 TATATAATATT
1 TATATAATATT
1381966 GTCATATTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
18 3 0.06
19 22 0.41
20 10 0.19
21 16 0.30
22 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (21 bp):
TATATAATATTTTTTATATTA
Found at i:1382122 original size:22 final size:22
Alignment explanation
Indices: 1382097--1382140 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1382087 TTGGATTTCC
1382097 CTATTTTATGAAGGAAAAATAA
1 CTATTTTATGAAGGAAAAATAA
1382119 CTATTTTATGAAGGAAAAATAA
1 CTATTTTATGAAGGAAAAATAA
1382141 ATAAGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.32
Consensus pattern (22 bp):
CTATTTTATGAAGGAAAAATAA
Found at i:1383321 original size:15 final size:15
Alignment explanation
Indices: 1383280--1383327 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1383270 TTAAATTTAA
* *
1383280 TAAAAAATAATATAT
1 TAAATAATAATATTT
1383295 TAAATTAA-AATATTT
1 TAAA-TAATAATATTT
*
1383310 TAAATAATAATAATT
1 TAAATAATAATATTT
1383325 TAA
1 TAA
1383328 TTATCTTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 3 0.11
15 23 0.82
16 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATAATAATATTT
Found at i:1383976 original size:34 final size:31
Alignment explanation
Indices: 1383912--1383977 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 31
1383902 TAAGGGTAAT
* **
1383912 ATTTAAAAAATATATAATTAATAATTTTTTA
1 ATTTAAAAAATATAAAATTAATAAAATTTTA
1383943 ATTTAATAAAATATAAAATTAAATATAAATTTTA
1 ATTTAA-AAAATATAAAATT-AATA-AAATTTTA
1383977 A
1 A
1383978 ATAATAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 6 0.21
32 12 0.41
33 4 0.14
34 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
ATTTAAAAAATATAAAATTAATAAAATTTTA
Found at i:1395169 original size:64 final size:64
Alignment explanation
Indices: 1395067--1395196 Score: 233
Period size: 64 Copynumber: 2.0 Consensus size: 64
1395057 CCACTAACAT
*
1395067 CTTTAGGTAACTAAAGCTAAATAAAACACAATCAAACATAAGTTAATGCACTGTTTTGTTGTCA
1 CTTTAGGTAACTAAAGCTAAAGAAAACACAATCAAACATAAGTTAATGCACTGTTTTGTTGTCA
**
1395131 CTTTAGGTAACTAAAGCTAAAGAAAACACAATTTAACATAAGTTAATGCACTGTTTTGTTGTCA
1 CTTTAGGTAACTAAAGCTAAAGAAAACACAATCAAACATAAGTTAATGCACTGTTTTGTTGTCA
1395195 CT
1 CT
1395197 CTTACTAAGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.32
Consensus pattern (64 bp):
CTTTAGGTAACTAAAGCTAAAGAAAACACAATCAAACATAAGTTAATGCACTGTTTTGTTGTCA
Found at i:1395221 original size:64 final size:64
Alignment explanation
Indices: 1395079--1395217 Score: 190
Period size: 64 Copynumber: 2.1 Consensus size: 64
1395069 TTAGGTAACT
* * **
1395079 AAAGCTAAATAAAACACAATCAAACATAAGTTAATGCACTGTTTTGTTGTCACTTTAGGTAACT
1 AAAGCTAAAGAAAACACAATCAAACATAAGTTAATGCACTGTTTTGTTGTCACTTTAGCTAAAA
**
1395143 AAAGCTAAAGAAAACACAATTTAACATAAGTTAATGCACTGTTTTGTTGTCACTCTTA-CTAAGA
1 AAAGCTAAAGAAAACACAATCAAACATAAGTTAATGCACTGTTTTGTTGTCACT-TTAGCTAA-A
1395207 A
64 A
1395208 AATAGCTAAA
1 AA-AGCTAAA
1395218 AAACGACAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 54 0.82
65 5 0.08
66 7 0.11
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (64 bp):
AAAGCTAAAGAAAACACAATCAAACATAAGTTAATGCACTGTTTTGTTGTCACTTTAGCTAAAA
Found at i:1396594 original size:20 final size:17
Alignment explanation
Indices: 1396559--1396613 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
1396549 TTCATAAATA
1396559 AATTAAAAAAATATTTT
1 AATTAAAAAAATATTTT
*
1396576 AATTAATAAATAATAATTT
1 AATTAA-AAA-AATATTTT
1396595 AA--AAAAATAA-ATTTT
1 AATTAAAAA-AATATTTT
1396610 AATT
1 AATT
1396614 TTACCATAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 8 0.25
18 3 0.09
19 9 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTAAAAAAATATTTT
Found at i:1397250 original size:11 final size:11
Alignment explanation
Indices: 1397234--1397294 Score: 81
Period size: 11 Copynumber: 5.6 Consensus size: 11
1397224 AATATATTGA
*
1397234 TATATTTAAAT
1 TATATTTATAT
1397245 TATATTTATAT
1 TATATTTATAT
1397256 TATATTTATAT
1 TATATTTATAT
*
1397267 TATATTATATTT
1 TATATT-TATAT
1397279 TATATTT-TA-
1 TATATTTATAT
1397288 TATATTT
1 TATATTT
1397295 TTAATTATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
9 7 0.15
10 1 0.02
11 28 0.61
12 10 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1397254 original size:17 final size:18
Alignment explanation
Indices: 1397244--1397295 Score: 76
Period size: 16 Copynumber: 3.1 Consensus size: 18
1397234 TATATTTAAA
1397244 TTATATTTATATTATA-T
1 TTATATTTATATTATATT
1397261 TTATA-TTATATTATATT
1 TTATATTTATATTATATT
1397278 TTATATTT-TA-TATATT
1 TTATATTTATATTATATT
1397294 TT
1 TT
1397296 TAATTATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
16 18 0.55
17 13 0.39
18 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATTTATATTATATT
Found at i:1397260 original size:5 final size:5
Alignment explanation
Indices: 1397226--1397290 Score: 55
Period size: 5 Copynumber: 13.0 Consensus size: 5
1397216 TAACTTTTAA
*
1397226 TATAT TGATA- TAT-T TAAAT TATATT TATAT TATATT TATAT TATAT
1 TATAT T-ATAT TATAT TATAT TATA-T TATAT TATA-T TATAT TATAT
* *
1397272 TATAT TTTA- TATTT TATAT
1 TATAT TATAT TATAT TATAT
1397291 ATTTTTAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
4 6 0.12
5 29 0.60
6 13 0.27
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:1397265 original size:28 final size:29
Alignment explanation
Indices: 1397233--1397302 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
1397223 TAATATATTG
1397233 ATATATTTAAATTATA-TTTATATTATAT
1 ATATATTTAAATTATATTTTATATTATAT
* * *
1397261 TTATA-TTATATTATATTTTATATTTTAT
1 ATATATTTAAATTATATTTTATATTATAT
*
1397289 ATAT-TTTTAATTAT
1 ATATATTTAAATTAT
1397303 TTATCTTGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
ATATATTTAAATTATATTTTATATTATAT
Found at i:1397271 original size:16 final size:16
Alignment explanation
Indices: 1397244--1397294 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
1397234 TATATTTAAA
1397244 TTATATTTATATTATAT
1 TTATA-TTATATTATAT
1397261 TTATATTATATTATATT
1 TTATATTATATTATA-T
*
1397278 TTATATTTTA-TATAT
1 TTATATTATATTATAT
1397293 TT
1 TT
1397295 TTAATTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 3 0.09
16 14 0.44
17 15 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTATATTATAT
Found at i:1397296 original size:17 final size:17
Alignment explanation
Indices: 1397207--1397297 Score: 60
Period size: 17 Copynumber: 5.0 Consensus size: 17
1397197 ATTTATGATT
*
1397207 TATTTTATATAACTTTTAA
1 TATTTTATAT-A-TTTTTA
*
1397226 TATATTGATATATTTAAATTA
1 TAT-TTTATATATTT---TTA
*
1397247 TA-TTTATATTATATTTA
1 TATTTTATA-TATTTTTA
*
1397264 TATTATAT-TATATTTTA
1 TATTTTATATAT-TTTTA
1397281 TATTTTATATATTTTTA
1 TATTTTATATATTTTTA
1397298 ATTATTTATC
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
16 3 0.05
17 21 0.37
18 10 0.18
19 9 0.16
20 10 0.18
21 4 0.07
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (17 bp):
TATTTTATATATTTTTA
Found at i:1398086 original size:2 final size:2
Alignment explanation
Indices: 1398079--1398110 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1398069 CCAGATTAAA
1398079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1398111 AGATCAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1399384 original size:22 final size:23
Alignment explanation
Indices: 1399356--1399422 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
1399346 TTTTTCTTTA
1399356 AAAAAATTTATAATTTAA-AAAT
1 AAAAAATTTATAATTTAATAAAT
*
1399378 AAAAAA-TTATAA-ATAATTAAAT
1 AAAAAATTTATAATTTAA-TAAAT
* *
1399400 AAAAATTTTA-AATTTATTAAAT
1 AAAAAATTTATAATTTAATAAAT
1399422 A
1 A
1399423 TTCACTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 3 0.08
21 6 0.16
22 23 0.62
23 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAAATTTATAATTTAATAAAT
Found at i:1399403 original size:21 final size:22
Alignment explanation
Indices: 1399353--1399422 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 22
1399343 ACTTTTTTCT
* *
1399353 TTAAA-AAAATTTATAATTTAA
1 TTAAATAAAAATTATAAATTAA
1399374 --AAATAAAAAATTATAAA-TAA
1 TTAAAT-AAAAATTATAAATTAA
* *
1399394 TTAAATAAAAATTTTAAATTTA
1 TTAAATAAAAATTATAAATTAA
1399416 TTAAATA
1 TTAAATA
1399423 TTCACTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
21 21 0.52
22 13 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAATAAAAATTATAAATTAA
Found at i:1400881 original size:14 final size:14
Alignment explanation
Indices: 1400864--1400912 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1400854 TTTAAAATAA
1400864 ATTATTAAAAAATT
1 ATTATTAAAAAATT
*
1400878 ATTAATT-TAAAATAT
1 ATT-ATTAAAAAAT-T
*
1400893 ATTATTAAAATATT
1 ATTATTAAAAAATT
1400907 ATTATT
1 ATTATT
1400913 TTGAGTGAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTATTAAAAAATT
Found at i:1400896 original size:29 final size:30
Alignment explanation
Indices: 1400849--1400914 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 30
1400839 TAAATTAGTG
1400849 TTAATTTTAAAATAAATTATTAAAAAATTA
1 TTAATTTTAAAATAAATTATTAAAAAATTA
* *
1400879 TTAA-TTTAAAATATATTATTAAAATATTA
1 TTAATTTTAAAATAAATTATTAAAAAATTA
1400908 TT-ATTTT
1 TTAATTTT
1400915 GAGTGAGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.85
30 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TTAATTTTAAAATAAATTATTAAAAAATTA
Found at i:1400959 original size:32 final size:32
Alignment explanation
Indices: 1400923--1400993 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1400913 TTGAGTGAGC
*
1400923 AAAAATCGTTA-AATTAACTAATAAATTTATGT
1 AAAAATCGTTATAA-TAACTAATAAATTTATAT
* *
1400955 AAAAATCGTTATAATAATTAATCAATTTATAT
1 AAAAATCGTTATAATAACTAATAAATTTATAT
1400987 AAAAATC
1 AAAAATC
1400994 ACTAAAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (32 bp):
AAAAATCGTTATAATAACTAATAAATTTATAT
Found at i:1401197 original size:19 final size:19
Alignment explanation
Indices: 1401136--1401203 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
1401126 TTATTTTAAT
*
1401136 ATTATAATATTATATATATA
1 ATTATAATATTA-ATATAAA
* *
1401156 TTTTTAA-ATTAATATAAA
1 ATTATAATATTAATATAAA
*
1401174 ATTATATTATTAATA-AAA
1 ATTATAATATTAATATAAA
1401192 ATTTATAATATT
1 A-TTATAATATT
1401204 CTAAATTAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 14 0.36
19 20 0.51
20 5 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTATAATATTAATATAAA
Found at i:1401385 original size:13 final size:13
Alignment explanation
Indices: 1401369--1401397 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1401359 TAGTTTAATT
1401369 ATTTAAATTAAAA
1 ATTTAAATTAAAA
1401382 ATTTAAATTAAAA
1 ATTTAAATTAAAA
1401395 ATT
1 ATT
1401398 ATAATAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTTAAATTAAAA
Found at i:1401610 original size:14 final size:14
Alignment explanation
Indices: 1401591--1401640 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
1401581 TTACTAATCA
1401591 AAATAATAATATTT
1 AAATAATAATATTT
*
1401605 AAATAAT-TTATTTT
1 AAATAATAATA-TTT
1401619 AAATTAATAATATTT
1 AAA-TAATAATATTT
*
1401634 TAATAAT
1 AAATAAT
1401641 TTATTATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.07
14 17 0.57
15 9 0.30
16 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATAATAATATTT
Found at i:1401632 original size:29 final size:29
Alignment explanation
Indices: 1401594--1401650 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1401584 CTAATCAAAA
*
1401594 TAATAATATTTAAATAATTTATTTTAAAT
1 TAATAATATTTAAATAATTTATTATAAAT
*
1401623 TAATAATATTTTAATAATTTATTATAAA
1 TAATAATATTTAAATAATTTATTATAAA
1401651 ACTTACACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TAATAATATTTAAATAATTTATTATAAAT
Found at i:1418698 original size:2 final size:2
Alignment explanation
Indices: 1418691--1418723 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1418681 ACTTGTTTAT
1418691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1418724 GCATTGTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1425753 original size:18 final size:20
Alignment explanation
Indices: 1425716--1425756 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
1425706 TAATCACATA
*
1425716 ATTTAAAATTTTATTTTATT
1 ATTTAAAATTATATTTTATT
1425736 ATTT-AAATTATA-TTTATT
1 ATTTAAAATTATATTTTATT
1425754 ATT
1 ATT
1425757 ATTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 7 0.35
20 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTAAAATTATATTTTATT
Found at i:1425785 original size:21 final size:20
Alignment explanation
Indices: 1425732--1425813 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 20
1425722 AATTTTATTT
*
1425732 TATTATTTAAATTATATTTAT-
1 TATTATTTAAA--AAATTTATA
1425753 TATTATTTTTAAAAAATTTATA
1 TATTA--TTTAAAAAATTTATA
*
1425775 TATTATGTT--AATATTTATA
1 TATTAT-TTAAAAAATTTATA
1425794 TATT-TTATAAATAAATTTAT
1 TATTATT-TAAA-AAATTTAT
1425814 TTTTTATTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
17 1 0.02
18 2 0.04
19 13 0.26
20 2 0.04
21 21 0.42
22 5 0.10
23 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (20 bp):
TATTATTTAAAAAATTTATA
Found at i:1425806 original size:19 final size:18
Alignment explanation
Indices: 1425745--1425806 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 18
1425735 TATTTAAATT
1425745 ATATTTATTATTATTTTTAAA
1 ATATTTA-TA-TATTTTT-AA
*
1425766 AAATTTATATATTATGTT-A
1 ATATTTATATATT-T-TTAA
1425785 ATATTTATATATTTTATAA
1 ATATTTATATATTTT-TAA
1425804 ATA
1 ATA
1425807 AATTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
17 1 0.03
18 2 0.06
19 21 0.60
20 3 0.09
21 8 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATATTTATATATTTTTAA
Found at i:1425849 original size:10 final size:10
Alignment explanation
Indices: 1425830--1425863 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1425820 TTATGTAAAT
1425830 ATTAATTTAA
1 ATTAATTTAA
*
1425840 ATTAAATTAA
1 ATTAATTTAA
*
1425850 ATTGATTTAA
1 ATTAATTTAA
1425860 ATTA
1 ATTA
1425864 TAAAAATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (10 bp):
ATTAATTTAA
Done.